Sending multiple REST commands over the same URL connection

Question

[yaronore]

Hello,

I am using Ensemble REST API to retrieve genomic coordinates based on positions in CDNA transcripts. The retrieval works, but it is very slow since I am doing it for thousands and millions of positions.

Is there an easy way to speed it up? can i send multiple requests over the same REST command or URL connection?

I am using JAVA and following the example given in Ensemble REST API documentation.

Thanks, Yaron

Answer 1

[sndrtj]

Generally, you can't, unless the specific API endpoint provides a method for such bulk requests. For some endpoints, the Ensembl REST API provides a POST method that allows such bulk queries. However, that's actually not very RESTful, since POST requests should usually result in the creation of some entity.

[yaronore]

Thanks for the reply.

So, is there another efficient way to convert cDNA positions to genomic coordinates?

Answer 2

[Alex Reynolds]

Instead of using remote REST requests, you might look at tools like BLAT or similar to do alignments in bulk on your own system. I think you can do multiple requests to a local BLAT server, using UCSC's server as a test. If that works, you can set up a local server and run the searches you need with fewer restrictions.

Answer 3

[Jean-Karim Heriche]

The best solution in my view would be to use a local copy of the EnsEMBL MySQL database and query it with the perl API.